Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

I m trying to do that! I ll let you know! thank you again in the mean time Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

If you were to delete everything and run again do you get the same error? Peace, Matt. From: "Mandelli, Maria Luisa" > Date: Wednesday, June 28, 2017 at 6:18 PM To: Matt Glasser >,

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

this is the version freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP and yes I m running the HCP Pipelines Maria Luisa Mandelli, PhD Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

That’s weird as I change the subject directory in the pipelines but don’t normally have this error. FreeSurfer just makes a symlink. What version of FreeSurfer are you using? Are you calling it using the HCP Pipelines? Peace, Matt. From: "Mandelli, Maria Luisa"

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Hi!thank you for your help! the error is in the log file Invalid argument ERROR reading /mnt/macdata/groups/language/malu-cloud/HCP_project/Pipelines_ExampleData/subjects/hcp350014/T1w/fsaverage/label/lh.BA1.label Linux mmandelli-vm 3.2.0-126-virtual #169-Ubuntu SMP Fri Mar 31 14:47:56 UTC

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Perhaps I missed it but I don’t actually see the error messages you are getting. Peace, Matt. From: > on behalf of "Timothy B. Brown" > Organization: Washington

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Hi Maria, My bet is that the error you are seeing is coming from the last call to recon-all in the FreeSurferPipeline.sh script. This would be in the statements that look like: #Final Recon-all Steps log_Msg "Final Recon-all Steps" recon-all -subjid $SubjectID -sd $SubjectDIR

Re: [HCP-Users] Behavioral performance data

Hi Kristina, Are you talking about the in-scanner performance data for the tfMRI tasks? Per run (RL or LR) in-scanner reaction time (RT) and accuracy (ACC) measures are available in each subject's tfMRI data in a {TASK}_Stats.csv file in the run specific task directory :

Re: [HCP-Users] Libnetcdf.so.6 error during mris_make_surfaces

Hi Lisa, Sorry for the delayed response. I've been working on a solution to the problem you raised. As you noted, the libnetcdf.so.6 file is no longer available at the places previously suggested. Please try the following: 1. Install the hdf5 library files that are prerequisites for

[HCP-Users] Job Openings: Software Engineers (2) on CCF Team

Hi Everyone, We are looking for two extraordinary software engineers to join the Human Connectome Project as part of the Connectome Coordination Facility team. We hope to fill the positions soon and look forward to hearing from you. Please see the attached abridged job descriptions. Full job

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Hi!I installed the freesurfer-hcp and I got an error in the Freesurfer pipeline here...in the label directory I dont see the file that the script is looking for! (lh.BA1.label) $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local/freesurfer/bin/recon-all PWD

[HCP-Users] Behavioral performance data

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